celegans.pe file not found

pursue9190 commented 6 years ago

When I run sga-align --name celegans.pe assemble.m75-contigs.fa s_6_1.fastq.gz s_6_2.fastq.gz

Who can help me ? Thanks

jts commented 6 years ago

Can you send the full error message?

Jared

pursue9190 commented 6 years ago

:~/tvelvet$ /home/ubuntu/sga_master/src/bin/sga-align --name celegans.pe assemble.m75-contigs.fa s_6_1.fastq.gz s_6_2.fastq.gz assemble.m75-contigs.fa ['s_6_1.fastq.gz', 's_6_2.fastq.gz']

Tasks which will be run:

Task enters queue = 'indexContigs' bwa index assemble.m75-contigs.fa /bin/sh: 1: bwa: not found Completed Task = 'indexContigs' Task enters queue = 'prepareReads' Completed Task = 'prepareReads' Task enters queue = 'alignReads' bwa aln -o 0 -t 1 assemble.m75-contigs.fa s_6_1.fastq.gz > s_6_1.fastq.assemble.m75-contigs.bwsai /bin/sh: 1: bwa: not found bwa aln -o 0 -t 1 assemble.m75-contigs.fa s_6_2.fastq.gz > s_6_2.fastq.assemble.m75-contigs.bwsai /bin/sh: 1: bwa: not found bwa sampe -s assemble.m75-contigs.fa s_6_1.fastq.assemble.m75-contigs.bwsai s_6_2.fastq.assemble.m75-contigs.bwsai s_6_1.fastq.gz s_6_2.fastq.gz | samtools view -Sb -o celegans.pe.bam - /bin/sh: 1: bwa: not found /bin/sh: 1: samtools: not found Completed Task = 'alignReads' Task enters queue = 'sortBAM' Traceback (most recent call last): File "/home/ubuntu/sga_master/src/bin/sga-align", line 162, in pipeline_run([sortBAM]) File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5916, in pipeline_run raise job_errors ruffus.ruffus_exceptions.RethrownJobError:

Original exception:

Exception #1
  '<class 'ruffus.ruffus_exceptions.RethrownJobError'>

    Exceptions generating parameters for

    task = 'sortBAM'

Original exception:

    Exception #1
      'ruffus.ruffus_exceptions.MissingInputFileError(    

        No way to run job: Input file 'celegans.pe.bam' does not exist)' raised in ...
       Task = def sortBAM(...):

    Traceback (most recent call last):
      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5118, in parameter_generator
        job_history, verbose_abbreviated_path):
      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 4945, in job_needs_to_run
        check_input_files_exist(*params)
      File "/usr/local/lib/python2.7/dist-packages/ruffus/file_name_parameters.py", line 399, in check_input_files_exist
        "Input file '%s' does not exist" % f)
    MissingInputFileError:     

        No way to run job: Input file 'celegans.pe.bam' does not exist

    ' raised in ...
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5887, in pipeline_run
    verbose)
  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5283, in fill_queue_with_job_parameters
    for params in job_parameters:
  File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5215, in parameter_generator
    raise errt
RethrownJobError: 

    Exceptions generating parameters for

    task = 'sortBAM'

Original exception:

    Exception #1
      'ruffus.ruffus_exceptions.MissingInputFileError(    

        No way to run job: Input file 'celegans.pe.bam' does not exist)' raised in ...
       Task = def sortBAM(...):

    Traceback (most recent call last):
      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 5118, in parameter_generator
        job_history, verbose_abbreviated_path):
      File "/usr/local/lib/python2.7/dist-packages/ruffus/task.py", line 4945, in job_needs_to_run
        check_input_files_exist(*params)
      File "/usr/local/lib/python2.7/dist-packages/ruffus/file_name_parameters.py", line 399, in check_input_files_exist
        "Input file '%s' does not exist" % f)
    MissingInputFileError:     

        No way to run job: Input file 'celegans.pe.bam' does not exist

jts commented 6 years ago

These are the important errors:

/bin/sh: 1: bwa: not found
/bin/sh: 1: samtools: not found

You need to have bwa and samtools installed.

pursue9190 commented 6 years ago

Thanks for your help,I solved this problem.

pursue9190 commented 6 years ago

What about this?

leted Task = 'sortBAM'

/home/ubuntu/sga_master/src/bin/sga-bam2de.pl -n 5 --prefix libPE celegans.pe.bam abyss-fixmate -h libPE.tmp.hist celegans.pe.bam | samtools view -Sb - > libPE.diffcontigs.bam [samopen] SAM header is present: 3193 sequences. Mateless 0 Unaligned 288422 2.03% Singleton 2046151 14.4% FR 11595602 81.6% RF 3 2.11e-05% FF 3 2.11e-05% Different 284143 2% Total 14214324 awk '$2 >= 3' libPE.tmp.hist > libPE.hist samtools sort -@1 -o libPE.diffcontigs.sorted.bam libPE.diffcontigs.bam open: No such file or directory [bam_sort_core] fail to open file libPE.diffcontigs.sorted.bam DistanceEst -s 200 --mind -99 -n 5 -k 99 -j 1 -o libPE.de libPE.hist -l 30 libPE.diffcontigs.sorted.bam error: `libPE.diffcontigs.sorted.bam': No such file or directory
/home/ubuntu/sga_master/src/bin/sga-astat.py -m 200 celegans.pe.refsort.bam Reading alignments from celegans.pe.refsort.bam [E::hts_open_format] Failed to open file celegans.pe.refsort.bam Traceback (most recent call last): File "/home/ubuntu/sga_master/src/bin/sga-astat.py", line 76, in bamFile = pysam.Samfile(bamFilename, "rb") File "pysam/libcalignmentfile.pyx", line 729, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 919, in pysam.libcalignmentfile.AlignmentFile._open IOError: [Errno 2] could not open alignment file celegans.pe.refsort.bam: No such file or directory
sga scaffold -m 200 --pe libPE.de -a libPE.astat -o scaffolds.n5.scaf assemble.m75-contigs.fa Reading distance estimates from libPE.de Error: could not open libPE.de for read
sga scaffold2fasta -m 200 -a assemble.m75-graph.asqg.gz -o scaffolds.n5.fa -d 1 --use-overlap --write-unplaced scaffolds.n5.scaf Graph best: 0 Graph unique: 1 Find overlaps: 4 Deleted edges for 0 super repetitive vertices Warning: removed 4 duplicate edges Vertices: 3193 Edges: 8884 Islands: 21 Tips: 102 Monobranch: 1420 Dibranch: 510 Simple: 2610 Num scaffolds: 0 Num gaps attempted: 0 Num gaps resolved: 0 Num gaps resolved by graph walk: 0 Num graph walks failed because of too many solutions: 0 Num graph walks failed because of no path: 0 Num gaps resolved by overlap: 0 Num overlaps failed: 0

pursue9190 commented 6 years ago

/home/ubuntu/sga_master/src/bin/sga-bam2de.pl -n 5 --prefix libPE celegans.pe.bam abyss-fixmate -h libPE.tmp.hist celegans.pe.bam | samtools view -Sb - > libPE.diffcontigs.bam [samopen] SAM header is present: 3193 sequences. Mateless 0 Unaligned 288422 2.03% Singleton 2046151 14.4% FR 11595602 81.6% RF 3 2.11e-05% FF 3 2.11e-05% Different 284143 2% Total 14214324 awk '$2 >= 3' libPE.tmp.hist > libPE.hist samtools sort -@1 -o libPE.diffcontigs.sorted.bam libPE.diffcontigs.bam open: No such file or directory

jts commented 6 years ago

what version of samtools are you using?

pursue9190 commented 6 years ago

samtools is already the newest version (0.1.19-1ubuntu1).

pursue9190 commented 6 years ago

version (0.1.19-1ubuntu1).

jts commented 6 years ago

That is a very old version, the newest is 1.8:

https://github.com/samtools/samtools/releases/tag/1.8

Can you try 1.8?

pursue9190 commented 6 years ago

Thank you very much ,I tried it and the problem was solved.

jts commented 6 years ago

Great, glad it is working.

jts / sga

celegans.pe file not found #151